We assessed the environmental quality of the Odiel-Tinto estuary, one of the most polluted in the world, by analysing the spatial variation of subtidal soft-bottom crustacean assemblages from 2000 to 2016. Our primary goal was to evaluate whether corrective measures implemented since 1986 have resulted in significant ecological improvement. The assemblages were structured according to the natural gradient from the estuary to the marine environment. Throughout the study, the assemblages exhibited low species richness and abundance (e.g., over 3 species and 180 individuals/m2 in the inner areas; 19 species and 510 individuals/m2 in the mouth zone). However, 2016 saw an increase in both species number and total abundance (e.g., over 5 and 24 species in the inner and mouth areas, respectively). Despite these observations, the Odiel-Tinto system harboured fewer species (24 species) compared to nearby estuaries like the Guadiana and Guadalquivir (over 50 species). Although there were signs of changes in the estuary over the sampling periods (e.g., a slight increase in richness and diversity in 2016 compared to 2002 and 2004), these fluctuations are likely characteristic of a highly dynamic environment rather than indications of genuine ecological recovery. These findings highlight the need for a long-term monitoring program, which should also encompass intertidal mudflats due to their higher density and biomass, easy accessibility, and reduced exposure to the impacts of recurrent maintenance dredging of the navigation channel.