The importance of zooplankton as an indicator of ecosystem health and climate change is widely accepted, but remains an understudied component of many estuarine ecosystems. In 2008, we initiated a monthly zooplankton monitoring program at the Padilla Bay National Estuarine Research Reserve (NERR) to explore temporal and spatial patterns in abundance and community composition. Samples were collected at two sites located in channels draining eelgrass covered flats, and a third located in deep (20 m) water well beyond the subtidal edge of the eelgrass beds. Water quality parameters (i.e. temperature, salinity) and nutrient concentrations were also measured at each of these sites. Analysis of these data over an 8 year period reveal tremendous seasonal, interannual and spatial variability in community composition. Strong seasonal transitions of the dominant plankton groups (copepods, copepod nauplii, and larvaceans) at the deep water site were found. However, these patterns were disrupted in 2014 when Padilla Bay and the greater regional area experienced its highest temperatures, lowest salinities, and a positive PDO index. Despite these co-occurring anomalies, paired measures of water quality parameters were not good predictors of abundance or shifting community composition. Accordingly, we explore the effect of time lags and integrating water quality parameters over multiple temporal scales to help identify what regulates zooplankton communities in Padilla Bay NERR. Additionally, we explore the phenological shifts of the spring and fall peaks in zooplankton abundance in relation to changing environmental factors and the impact theses shifts may have on the food web and larval recruitment in Padilla Bay