Salt marshes support high biodiversity and provide essential ecosystem services, yet are increasingly threatened by climate change, reduced freshwater input, and human activities. This pilot study examined the physico-chemical characteristics and biodiversity of the Palud salt marsh in Istria, Croatia, during July 2021, focusing on phytoplankton, zooplankton, and macrozoobenthos communities across different habitats. The results show that while parameters like water temperature and pH remained stable, dissolved oxygen and nutrient levels fluctuated significantly. Water depth decreased due to drought and tidal oscillations, affecting salinity and nutrient concentrations. Phytoplankton communities were dominated by Bacillariophyta, with Cryptophyta, particularly Cryptomonas sp., having the highest abundance. Zooplankton communities were dominated by Rotifera, especially Brachionus plicatilis, while the macrozoobenthos communities were dominated by Ostracoda, with some variation in gastropod and chironomid abundance across sites. These findings indicate the dynamic nature of plankton and benthos communities in response to changing water levels in the Palud marsh. This study highlights the need for targeted conservation strategies to preserve the ecological integrity of Mediterranean salt marshes. Sustainable management practices must account for water level fluctuations, the role of aquatic vegetation, and the resilience of these ecosystems, emphasizing their importance in supporting biodiversity and ecosystem services in the face of environmental change.