In order to use sustainable methodologies in the exploration of oil and gas in lentic aquatic systems, a modified methodology (MTR) was implemented in each phase. Simultaneously, water quality, sediment, and organisms were evaluated to detect possible effects. Results included non-compaction of the sediment and less resuspension of dissolved solids and nutrients. Effects such as the increase in blue-green algae and the decrease in benthic macroinvertebrates showed rapid recovery (<15 days) as well as the resuspension of sulfates. Finally, MTR Methodology was feasible, of low magnitude, punctual effect, and rapid recovery for the intervened aquatic systems.