These are the data used in the analyses described in the paper titled "Seasonal dynamics of faunal diversity and population ecology in an estuarine seagrass bed", accepted at Estuaries and Coasts. We acknowledge the tangata whenua for the rohe in which these data were collected, Ngāi Tārewa and Ngāti Īrakehu. We thank the Akaroa Taiāpure for their support of this research. The data included are: Raw count data of taxa for each tow, associated with additional metadata including the date of collection, tow coordinates, and estimated seagrass cover (MonthlyRawSampling_Duvauchelle_2020.csv). This data was put through cleaning steps outlined in the file docs/dataCleaning.Rmd prior to being used in any analyses. The cleaned community composition data (cleanedCommunity.csv), output from docs/dataCleaning.Rmd and used in the downstream community and population analyses. The GPS coordinates for the tows (gpsdat.csv). These were extracted from the raw data in the data cleaning process. NZsyngnathids_measurements.csv contains the measurements of the pipefish from images. These data also underwent a cleaning process documented in docs/dataCleaning.Rmd. The cleaned pipefish trait data (pipefishTraits.csv), output from docs/dataCleaning.Rmd and used in the downstream population analysis documented in docs/populationAnalyses.Rmd.