The data presents field sampling undertaken at Nazareth tidal flat and marsh located west of Rimouski on the southern shore of Lower St. Lawrence Estuary (Canada). Three cross shore transects (A, B, C) were established with a total of 29 stations covering high marsh, low marsh, mudflat and sandflat. Small sediment cores (n=3) were taken for quantifying EPS (EPS SALINE & EPS EDTA) and pigment concentration (Chlorophyll a and Phaeopigments) using 60 ml syringes (36 mm ϕ). Measurements for the annual changes in Chl a and EPS concentrations were conducted in three consecutive summers on transects A, B, C in 2016 (9-11 August), 2017 (23-25 August) and on transect B in 2018 (6 September).