We used social network analysis (SNA) to identify the types of water-related conflicts between the users and members of the institutional arena of the Rio Mayo Irrigation District (RMID) within the ancestral territory of the Yoreme Mayo indigenous group in Sonora, northeastern Mexico. We combined ethnography with an analysis and visualization of bimodal networks that consisted of 118 users and their connections to the institutional arena’s 30 identified social actors who influence water management. Using a clustering algorithm, we identified four types of conflicts: (1) disputes between small- and large-scale farmers over (i) irrigation water and (ii) payments for water rights and land rental; (2) the struggle by large-scale farmers against the upper level of the water hierarchy, to obtain more water; (3) struggles by rural indigenous women against water providers, to conserve indigenous vernacular systems of managing water for domestic use; and (4) a “conflict” that turned out to be merely a structural remnant of the algorithm. We conclude that land- and water-grabbing in the RMID mainly affect indigenous small-scale farmers and that the combination of SNA and a clustering algorithm can identify the types of natural resource-related conflicts that might go undetected by other methodologies. However, SNA should in some cases be accompanied by a qualitative methodology.