Abstract Background Antimicrobial irrational use and poor disposal in the human and animal sectors promote antimicrobial resistance (AMR) in the environment. While AMR containment programmes in these sectors are well established, those in the Water and Environment sector still need to be established. We present Uganda’s experience in establishing AMR surveillance in the Water and Environment sector. Methodology A stepwise approach was employed. Governance structures were streamlined and sector-specific AMR surveillance guiding documents developed. The National Water Quality Reference Laboratory (NWQRL) infrastructure and microbiology capacity were enhanced to aid AMR surveillance. A passive and targeted active surveillance hybrid was employed to generate AMR data. Passive surveillance utilized remnants of water samples collected routinely for water quality monitoring while targeted active surveys were done at selected sites around Kampala and Wakiso districts. Results A sector-specific Technical Working Group of 10 members and focal persons are in place and providing strategic direction and linkage to the national AMR surveillance programme. The NWQRL is now at biosafety level 2 and conducting microbiology testing. Up to 460 samples were processed from August 2021 to March 2023 and 602 bacterial isolates were recovered, of which 399 (66%) and 203 (34%) were priority isolates and non-priority isolates respectively. Of the 399 priority isolates, 156 (39%), 140 (35%), 96 (24%), and 7 (2%) were Escherichia coli, Klebsiella, Enterococcus, and Salmonella species respectively. Escherichia coli showed resistance to ampicillin (79%), ciprofloxacin (29%), and ceftriaxone (29%). Similarly, Klebsiella species showed resistance to ampicillin (100%), ciprofloxacin (17%), and ceftriaxone (18%). Enterococcus species showed resistance to ciprofloxacin (52%), vancomycin (45%), and erythromycin (56%). Up to 27 % (n=160) of the recovered isolates exhibited multi and extensive drug resistance. Conclusion Initial efforts to establish and implement AMR surveillance in the water and environment sector have succeeded in streamlining governance and generating resistance data.