The assessment of pollution in poor regions remains a challenge for developing countries. Difficult access to and low availability of logistical conditions result in a lack of information on environmental quality in these regions. To provide information on heavy metals concentrations in water and sediments, samples were collected in seven sampling stations in São Marco Bay's harbor area, seasonally, from August 2017 to September 2018. Water samples were evaluated for temperature, turbidity, salinity, Eh, oxygen content, pH, phosphorus, total organic carbons, and heavy metals. In sediment samples, heavy metals' potentially mobilizable fractions were evaluated. In parallel, grain size, organic matter and redox potential were also analyzed. The average values of water and its physicochemical parameters revealed an unstratified environment with a great influence of ocean waters. High concentrations of metals were recorded in the water of sediment contamination. The present study suggested the high hydrodynamics and resulting coarser grain size accumulation as the cause for the relatively balanced environment conditions.