Coincident changes in abundance and behavior pose a challenge for interpreting abundance data from monitoring programs. In the San Francisco Estuary, long-term monitoring documented the declines of many species including the anadromous Longfin Smelt (Spirinchus thaleichthys). We identified seasonal patterns in reginal presence of Longfin Smelt through its life cycle using monitoring data and generalized additive modelling. We then investigated the year-to-year variability in the seasonal patterns of presence using functional data analysis (FDA). FDA separated the variability due to population size from variability due to differences in timing of presence. We found that Longfin Smelt have consistent seasonal distribution patterns and that two trawl types were needed to accurately describe those patterns. After accounting for variability due to year-class strength, shifts in the timing of presence were evident in three regions. The most variable period for the upstream regions Suisun Bay and West Delta was for age-0 fish in summer and for the downstream region Central Bay was for age-0 fish in late fall. This manifested as a delay in the typical fall re-occupation of upstream regions that comprise the study area for another monitoring study (Fall Midwater Trawl). Thus, a portion of the recent reductions in Fall Midwater Trawl abundance of Longfin Smelt resulted from changes in behavior rather than a decline in abundance. The presence of multiple monitoring surveys allowed analysis of distribution from one data set to aid interpretation of patterns in abundance from another monitoring survey. This study highlights how identifying portions of the life cycle with the most and least variability in distribution can help inform the types of management strategies that will be most effective. It also illustrates an analytical method that can be used to address the problem of confounded effects of abundance and behavior on patterns in monitoring data.