Removing sugarcane straw to increase bioenergy production can generate significant income to the industry. However, straw contributes to the regulation of soil functions and consequently supports the provision of ecosystem services, such as water flow regulation. Thus, straw removal may hinder the provision of these services, especially in mechanized sugarcane production systems, which have soil compaction problems due to machinery traffic. In this study, we assess a six-year experiment in Brazil with four rates of straw removal: 0 Mg ha−1 (TR), 5 Mg ha−1 (HR), 10 Mg ha−1 (LR), and 15 Mg ha−1 (NR) remaining straw. Using attributes, such as soil bulk density, porosity, water infiltration, runoff, saturated hydraulic conductivity and available water-holding capacity, as indicators of key soil functions, we calculated a soil-related ecosystem service (ES) index for water flow regulation provision. The ES index revealed that water flow regulation was low regardless of the straw management (0.56, 0.63, 0.64 and 0.60 for TR, HR, LR and NR, respectively). It can be a consequence of soil compaction caused by machinery traffic throughout the successive cycle, whose straw was unable to mitigate this issue. Thus, by the end of the sugarcane cycle (sixth ratoon), straw removal had little effect on soil physical and hydraulic indicators, and consequently had little impact on the provision of the soil-related ES associated with water flow regulation. Nevertheless, straw management should be planned to consider other functions and soil-related ES benefited by straw retention.