Picophytoplankton are vital components of the marine microbial food web. Being the smallest in the phytoplankton group, their short life cycles make them excellent bioindicators of environmental conditions. Given this, an investigation was conducted at the Kandla Port ecosystem (Latitude 23º 01' N; Longitude 70º 13' E) in the state of Gujarat, India to assess the response of picophytoplankton community structure to temporal and spatial environmental conditions. The sampling was conducted in July 2015, October-November 2015, and February 2016 at twenty-six stations. The results revealed a wide annual temperature range due to the study site's proximity to the Tropic of Cancer. The salinity ranged up to 40 while the turbulence caused by the macrotides resulted in highly turbid waters, especially during July due to precipitation. The picophytoplankton community was represented by picocyanobacteria (three sub-groups of Synechococcus) and picoeukaryotes (three sub-groups including Cryptophytes). The picocyanobacteria were abundant during the less turbid, warmer October-November period and lower during the cooler February period. The dominant Synechoccocus groups are associated positively with NH4+ and negatively with PO43-. The Cryptophytes were present during the warm and cool periods indicating tolerance to a wide range of temperature, salinity, and light. Their positive correlation with PO43- and NH4+ concentrations during February and October-November, respectively suggests a causal relationship. The picoeukaryotic group dominated the picophytoplankton community during the cooler period (February). The relative importance of the two picophytoplankton groups changed throughout the year exhibiting temporal niche segregation and hence establishing their role as bioindicators of temperature. •Picophytoplankton community as bioindicators of temporal temperature variability.•Limited studies on their response in macrotidal turbid coastal ecosystems.•Synechoccocus dominant in warm period and picoeukaryotes in cooler period.•Two groups’ exhibited temporal niche segregation.•Cryptophytes tolerant to wide temperature, salinity, and light ranges.