The objective of this study was to assess the perceived effectiveness of institutional support of the Bureau of Soils and Water Management (BSWM) to pilot Small Water Irrigation System Associations (SWISAs) in Luzon. SWISA is an association of organized farmer-beneficiaries of Small-Scale Irrigation Projects specifically for community-managed Small Water Impounding Project and Diversion Dam. Institutional support provided to SWISAs are facilitated by contracted CDOs assigned in regions. Correlational research design was used in the study. Of the 22 pilot SWISAs with 520 farmer members, 226 respondents were identified. The respondents were selected from the members of active pilot SWISAs with an operational irrigation system for at least three years. Based on the results of this study, as the level of participation of SWISA members in the organizational undertakings, operation and maintenance activities, and implementation of activity plans increases, the perception of effectiveness of BSWM’s institutional support to pilot SWISAs also increases. Moreover, as the level of understanding of CDOs of their roles in conducting organizational and monitoring activities, capacity enhancement, and coordinating activities increases, the perception on the effectiveness of the provided extension support also increases. Hence, generating the actual needs of farmers and the continuous strengthening of extension staff are necessary for the effective implementation of institutional program.