Abstract Identifying ecological niche filters that shape species community composition is a critical first step in understanding the relative contributions of deterministic and stochastic processes in structuring communities. Systems with harsh ecological filters often have a more deterministic basis to community structure. Although these filters are often treated as static, investigations into their stability through time are rare, particularly in combination with extreme forms of environmental change such as drought. We examined the richness and composition of aquatic macroinvertebrate communities from 36 ponds over 4 years during the onset of a megadrought to answer the following questions: (a) what are the relative influences of non‐native fish presence and pond permanence in structuring communities? And (b) how do the magnitudes of such filters vary through time? As predicted, fish presence had a strong, negative effect on both alpha and gamma diversity, lowering average invertebrate richness in pond communities by 23%. However, fish presence and sample year interacted to determine both richness and taxa composition: as drought conditions intensified, the effects of fish w
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