Long-term changes of the phytoplankton community and biomass in the subtropical shallow Patos Lagoon Estuary, Brazil

• Salinity variability is the main driver of water quality and phytoplankton variation
• Diatoms are the main phytoplankton group and determine chlorophyll a seasonality.
• Salinity fluctuations were filtered out by a novel decomposition tool, revealing:
• Strong inter annual variations, but no trends of chlorophyll a and diatoms.
• Increasing trends of N:P, cyanobacteria and dinoflagellates.

Seasonal and interannual changes (1993–2012) of water temperature and transparency, river discharge, salinity, water quality properties, chlorophyll a (chl-a) and the carbon biomass of the main taxonomical phytoplankton groups were evaluated at a shallow station (∼2 m) in the subtropical Patos Lagoon Estuary (PLE), Brazil. Large variations in salinity (0–35), due to a complex balance between Patos Lagoon outflow and oceanic inflows, affected significantly other water quality variables and phytoplankton dynamics, masking seasonal and interannual variability. Therefore, salinity effect was filtered out by means of a Generalized Additive Model (GAM). River discharge and salinity had a significant negative relation, with river discharge being highest and salinity lowest during July to October. Diatoms comprised the dominant phytoplankton group, contributing substantially to the seasonal cycle of chl-a showing higher values in austral spring/summer (September to April) and lowest in autumn/winter (May to August). PLE is a nutrient-rich estuary and the phytoplankton seasonal cycle was largely driven by light availability, with few exceptions in winter. Most variables exhibited large interannual variability. When varying salinity effect was accounted for, chl-a concentration and diatom biomass showed less irregularity over time, and significant increasing trends emerged for dinoflagellates and cyanobacteria. Long-term changes in phytoplankton and water quality were strongly related to variations in salinity, largely driven by freshwater discharge influenced by climatic variability, most pronounced for ENSO events. However, the significant increasing trend of the N:P ratio indicates that important environmental changes related to anthropogenic effects are undergoing, in addition to the hydrology in the PLE.