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Abstract In aquatic ecosystems, greater food web complexity is theorized to increase persistence and resilience of primary production to pulse disturbances, yet experimental evidence is limited. We simulated two storm‐induced pulse disturbances by adding nutrients (~ 3%–5% increase in ambient concentrations) to three ponds with low, intermediate, and high food web complexity and compared to reference ponds. We evaluated the ecological stability of primary production by quantifying persistence as the number of days it took chlorophyll‐aor ecosystem metabolism to deviate significantly from reference conditions and resilience as the time to recover to reference conditions following each disturbance. We also evaluated if a critical transition occurred following the disturbance. The high complexity pond did not significantly deviate from reference conditions following either nutrient pulse, suggesting high ecological stability. The intermediate complexity pond had lower stability, with persistence relatively consistent at 18 and 24 d after each nutrient pulse, and resilience trending toward a substantial increase from 23 d to less than a week before the experiment concluded. Stability was lowest in the low complexity pond where persistence decreased from 24 d to just 8 d and resilience decreased from 5 to 22 d. There was also evidence of a critical transition after the first pulse in the low complexity pond, but not for higher complexity ponds. This experiment provides strong support that food web connectivity and food chain length can aid in buffering aquatic ecosystems against increasing and intensifying by influencing persistence and resilience to repeated nutrient pulses.