diff --git a/public/app/features/dashboard-scene/panel-edit/PanelDataPane/ConnectionLines.tsx b/public/app/features/dashboard-scene/panel-edit/PanelDataPane/ConnectionLines.tsx
new file mode 100644
index 00000000000..9525af48ed2
--- /dev/null
+++ b/public/app/features/dashboard-scene/panel-edit/PanelDataPane/ConnectionLines.tsx
@@ -0,0 +1,177 @@
+import { css } from '@emotion/css';
+import { useLayoutEffect, useRef, useState } from 'react';
+
+import { GrafanaTheme2 } from '@grafana/data';
+import { useStyles2 } from '@grafana/ui';
+
+interface Connection {
+  from: string;
+  to: string;
+}
+
+interface ConnectionLinesProps {
+  connections: Connection[];
+}
+
+export function ConnectionLines({ connections }: ConnectionLinesProps) {
+  const styles = useStyles2(getStyles);
+  const [positions, setPositions] = useState<Map<string, DOMRect>>(new Map());
+  const containerRef = useRef<SVGSVGElement>(null);
+
+  // Update positions when cards change
+  useLayoutEffect(() => {
+    const updatePositions = () => {
+      const newPositions = new Map<string, DOMRect>();
+
+      // Find all cards by their data-card-id attribute
+      const cards = document.querySelectorAll('[data-card-id]');
+
+      cards.forEach((element) => {
+        const cardId = element.getAttribute('data-card-id');
+        if (cardId) {
+          const rect = element.getBoundingClientRect();
+          newPositions.set(cardId, rect);
+        }
+      });
+
+      setPositions(newPositions);
+    };
+
+    // Delay to ensure cards are rendered
+    const timeoutId = setTimeout(updatePositions, 100);
+
+    // Update on resize and scroll
+    window.addEventListener('resize', updatePositions);
+
+    const container = containerRef.current?.parentElement;
+    if (container) {
+      // Watch for scroll events
+      const scrollContainer = container.querySelector('[data-scrollcontainer]');
+      scrollContainer?.addEventListener('scroll', updatePositions);
+
+      // Watch for DOM changes
+      const observer = new MutationObserver(() => {
+        setTimeout(updatePositions, 50);
+      });
+      observer.observe(container, { childList: true, subtree: true });
+
+      // Watch for container resize (splitter changes)
+      const resizeObserver = new ResizeObserver(updatePositions);
+      resizeObserver.observe(container);
+
+      return () => {
+        clearTimeout(timeoutId);
+        window.removeEventListener('resize', updatePositions);
+        scrollContainer?.removeEventListener('scroll', updatePositions);
+        observer.disconnect();
+        resizeObserver.disconnect();
+      };
+    }
+
+    return () => {
+      clearTimeout(timeoutId);
+      window.removeEventListener('resize', updatePositions);
+    };
+  }, [connections]);
+
+  const containerRect = containerRef.current?.parentElement?.getBoundingClientRect();
+
+  if (!containerRect || connections.length === 0) {
+    return <svg ref={containerRef} className={styles.svg} />;
+  }
+
+  // Group connections by expression (each "to" card gets its own lane)
+  const lanesByExpression = new Map<string, Set<string>>();
+
+  connections.forEach((conn) => {
+    if (!lanesByExpression.has(conn.to)) {
+      lanesByExpression.set(conn.to, new Set());
+    }
+    const lane = lanesByExpression.get(conn.to)!;
+    lane.add(conn.from); // Add the referenced query
+    lane.add(conn.to); // Add the expression itself
+  });
+
+  // Convert to array of lanes
+  const activeLanes = Array.from(lanesByExpression.values());
+
+  // Find the rightmost edge of all cards
+  let maxCardRight = 0;
+  positions.forEach((rect) => {
+    const cardRight = rect.right - containerRect.left;
+    if (cardRight > maxCardRight) {
+      maxCardRight = cardRight;
+    }
+  });
+
+  const laneSpacing = 16; // Spacing between lanes (must match QueryTransformList.tsx)
+  const baseOffset = 24; // Offset from rightmost card (must match QueryTransformList.tsx)
+
+  return (
+    <svg ref={containerRef} className={styles.svg}>
+      {activeLanes.map((lane, laneIndex) => {
+        // Calculate Y positions for cards in this lane
+        const laneYPositions: number[] = [];
+        lane.forEach((cardId) => {
+          const cardRect = positions.get(cardId);
+          if (cardRect) {
+            laneYPositions.push(cardRect.top + cardRect.height / 2 - containerRect.top);
+          }
+        });
+
+        if (laneYPositions.length === 0) {
+          return null;
+        }
+
+        // Calculate swimlane X position for this lane (start from rightmost card edge)
+        const swimlaneX = maxCardRight + baseOffset + laneIndex * laneSpacing;
+
+        // Find min/max Y to draw the line only between connected points
+        const minY = Math.min(...laneYPositions);
+        const maxY = Math.max(...laneYPositions);
+
+        return (
+          <g key={laneIndex}>
+            {/* Vertical swimlane line */}
+            <line x1={swimlaneX} y1={minY} x2={swimlaneX} y2={maxY} className={styles.swimlane} />
+
+            {/* Connection points for cards in this lane */}
+            {Array.from(lane).map((cardId) => {
+              const cardRect = positions.get(cardId);
+
+              if (!cardRect) {
+                return null;
+              }
+
+              const pointY = cardRect.top + cardRect.height / 2 - containerRect.top;
+
+              return <circle key={cardId} cx={swimlaneX} cy={pointY} r={4} className={styles.point} />;
+            })}
+          </g>
+        );
+      })}
+    </svg>
+  );
+}
+
+const getStyles = (theme: GrafanaTheme2) => ({
+  svg: css({
+    position: 'absolute',
+    top: 0,
+    left: 0,
+    width: '100%',
+    height: '100%',
+    pointerEvents: 'none',
+    zIndex: 10,
+    overflow: 'visible',
+  }),
+  swimlane: css({
+    stroke: theme.colors.text.maxContrast,
+    strokeWidth: 2,
+    opacity: 0.3,
+  }),
+  point: css({
+    fill: theme.colors.text.maxContrast,
+    opacity: 0.8,
+  }),
+});
diff --git a/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformCard.tsx b/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformCard.tsx
index 7c4297f9827..73d3f538997 100644
--- a/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformCard.tsx
+++ b/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformCard.tsx
@@ -68,6 +68,7 @@ export const QueryTransformCard = memo(
         onClick={onClick}
         onKeyDown={handleKeyDown}
         data-testid={`${type}-card-${index}`}
+        data-card-id={'refId' in item ? item.refId : `transform-${index}`}
       >
         {/* Header with type and action icons */}
         <div
@@ -149,6 +150,7 @@ const getStyles = (theme: GrafanaTheme2) => {
 
   return {
     card: css({
+      position: 'relative',
       cursor: 'pointer',
       border: `1px solid ${theme.colors.border.weak}`,
       borderRadius: theme.shape.radius.default,
diff --git a/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformList.tsx b/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformList.tsx
index e7509b45d90..41e1844d7cb 100644
--- a/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformList.tsx
+++ b/public/app/features/dashboard-scene/panel-edit/PanelDataPane/QueryTransformList.tsx
@@ -1,5 +1,5 @@
 import { css } from '@emotion/css';
-import { memo } from 'react';
+import { memo, useMemo } from 'react';
 
 import { DataTransformerConfig, GrafanaTheme2 } from '@grafana/data';
 import { SceneDataQuery } from '@grafana/scenes';
@@ -7,6 +7,7 @@ import { ScrollContainer, Stack, useStyles2 } from '@grafana/ui';
 import { ExpressionQueryType } from 'app/features/expressions/types';
 
 import { AddDataItemMenu } from './AddDataItemMenu';
+import { ConnectionLines } from './ConnectionLines';
 import { QueryTransformCard } from './QueryTransformCard';
 
 export interface QueryTransformItem {
@@ -50,6 +51,41 @@ export const QueryTransformList = memo(
   }: QueryTransformListProps) => {
     const styles = useStyles2(getStyles);
 
+    // Detect connections between items
+    const connections = useMemo(() => {
+      const conns: Array<{ from: string; to: string }> = [];
+
+      items.forEach((item) => {
+        if (item.type === 'expression' && 'expression' in item.data && 'refId' in item.data) {
+          const expr = item.data;
+
+          if ('expression' in expr && typeof expr.expression === 'string' && 'type' in expr) {
+            const expressionType = expr.type;
+            const expressionString = expr.expression;
+
+            if (expressionType === 'math') {
+              // Math expressions: parse $A, $B, etc.
+              const matches = expressionString.matchAll(/\$(\w+)/g);
+              for (const match of matches) {
+                const refId = match[1];
+                conns.push({ from: refId, to: expr.refId });
+              }
+            } else if (expressionType === 'reduce' || expressionType === 'resample' || expressionType === 'threshold') {
+              // Reduce/Resample/Threshold: expression field is a single refId
+              if (expressionString) {
+                conns.push({ from: expressionString, to: expr.refId });
+              }
+            }
+            // TODO: Handle 'sql' and 'classic_conditions' types if needed
+          }
+        }
+      });
+
+      console.log('Detected connections:', conns);
+
+      return conns;
+    }, [items]);
+
     const getHandlers = (item: QueryTransformItem) => {
       switch (item.type) {
         case 'query':
@@ -75,10 +111,22 @@ export const QueryTransformList = memo(
       }
     };
 
+    // Calculate number of lanes for dynamic padding
+    const lanesByExpression = useMemo(() => {
+      const lanes = new Map<string, Set<string>>();
+      connections.forEach((conn) => {
+        if (!lanes.has(conn.to)) {
+          lanes.set(conn.to, new Set());
+        }
+      });
+      return lanes.size;
+    }, [connections]);
+
     return (
       <div className={styles.container}>
-        <div className={styles.scrollContainer}>
-          <ScrollContainer>
+        <ConnectionLines connections={connections} />
+        <ScrollContainer data-scrollcontainer>
+          <div className={lanesByExpression > 0 ? styles.contentWithConnections(lanesByExpression) : styles.content}>
             <Stack direction="column" gap={2}>
               {items.map((item) => (
                 <QueryTransformCard
@@ -98,8 +146,8 @@ export const QueryTransformList = memo(
                 onAddExpression={onAddExpression}
               />
             </Stack>
-          </ScrollContainer>
-        </div>
+          </div>
+        </ScrollContainer>
       </div>
     );
   }
@@ -108,19 +156,31 @@ export const QueryTransformList = memo(
 QueryTransformList.displayName = 'QueryTransformList';
 
 const getStyles = (theme: GrafanaTheme2) => {
+  const laneSpacing = 16; // Must match ConnectionLines.tsx
+  const baseOffset = 24; // Must match ConnectionLines.tsx
+  const extraPadding = 8; // Extra breathing room beyond the last lane
+
   return {
     container: css({
+      position: 'relative',
       display: 'flex',
       flexDirection: 'column',
       height: '100%',
       width: '100%',
       overflow: 'hidden',
     }),
-    scrollContainer: css({
+    content: css({
+      position: 'relative',
       padding: theme.spacing(2),
-      flex: 1,
-      minHeight: 0,
-      overflow: 'auto',
+      zIndex: 1,
     }),
+    contentWithConnections: (numLanes: number) =>
+      css({
+        position: 'relative',
+        padding: theme.spacing(2),
+        // Calculate exact space needed: base offset + (lanes * spacing) + extra padding
+        paddingRight: baseOffset + numLanes * laneSpacing + extraPadding,
+        zIndex: 1,
+      }),
   };
 };