During the last few decades, inputs of mercury (Hg) to the environment from anthropogenic sources have increased. The Ebro Delta is an important area of rice production in the Iberian Peninsula. Given the industrial activity and its legacy pollution along the Ebro river, residues containing Hg have been transported throughout the Ebro Delta ecosystems. Rice paddies are regarded as propitious environments for Hg methylation and its subsequent incorporation to plants and rice paddies' food webs. We have analyzed how Hg dynamics change throughout the rice cultivation season in different compartments from the paddies' ecosystems: soil, water, rice plants and fauna. Furthermore, we assessed the effect of different agricultural practices (ecological vs. conventional) associated to various flooding patterns (wet vs. mild alternating wet and dry) to the Hg levels in rice fields. Finally, we have estimated the proportion of methylmercury (MeHg) to total mercury in a subset of samples, as MeHg is the most bioaccumulable toxic form for humans and wildlife. Overall, we observed varying degrees of mercury concentration over the rice cultivation season in the different compartments. We found that different agricultural practices and flooding patterns did not influence the THg levels observed in water, soil or plants. However, Hg concentrations in fauna samples seemed to be affected by hydroperiod and we also observed evidence of Hg biomagnification along the rice fields' aquatic food webs.