What causes my tree stood in water after the yard flooded and now it looks sick?

Central Indiana's heavy clay and silty clay till holds water and drains slowly, so a single heavy rain leaves many yards flooded far longer than the storm lasted. Beyond weather, the usual human causes are grade changes that route runoff to a low spot, downspouts and sump discharges aimed at a tree, new hardscape shedding water, failed drain tile, irrigation on a clay-soil schedule, and compaction that removed the pore space before the flood ever arrived. Timing matters more than depth: flooding while the tree is dormant in winter is generally shrugged off, while the same water in June — tree transpiring, soil warm and biologically active — does the damage.