Sungai Juwana merupakan sungai terbesar dan terpanjang di Kota Pati. Berkembangnya kegiatan penduduk di Daerah Aliran Sungai (DAS) Juwana dapat mempengaruhi struktur komunitas dan distribusi ikan. Penelitian ini menggunakan rancangan eksplorasi dengan metode survei, dimana penetapan stasiun pengambilan sampel dengan purposive sampling. Penempatan stasiun didasarkan atas perkiraan beban pencemar yang masuk ke sungai dan kegiatan penangkapan ikan oleh nelayan di sepanjang sungai. Stasiun 1 berada di hulu sumber limbah pertanian, stasiun 2 berada di sumber limbah industri pabrik kacang, stasiun 3 berada di sumber limbah industri peleburan timah, stasiun 4 berada di hilir sumber limbah solar dari kapal nelayan (dekat muara). Pengambilan sampel dilakukan sebanyak 2 kali dengan selang waktu 2 minggu. Hasil penelitian ditemukan 17 jenis ikan terdiri dari 13 jenis family. Distribusi spesies ikan di sepanjang Sungai Juwana keanekaragamannya rendah dikarenakan tidak merata distribusi penyebarannya dan cenderung ada spesies yang mendominasi pada setiap stasiun penelitian. Berdasarkan kriteria tingkat pencemaran menunjukkan bahwa Sungai Juwana berada dalam kondisi tercemar ringan sampai dengan cukup berat.Juwana River is the largest and longest river in Pati. The activities of the population in Juwana watershed can affect the structure and distribution of fish communities. This study uses an exploration design with survey method, where the determination of sampling stations was purposive sampling. The stations were determined based on the estimated pollutant loads entering the river and fishing activities along the river. Station 1 was located upstream source of agricultural waste , industrial waste station 2 was the industrial waste and source bean plant, station 3 was source of waste tin smelting industry, station 4 in the downstream diesel fuel sources of waste from fishing boats ( near the liver ). Sampling was done 2 times with an interval of 2 weeks. The research found 17 species of fish consisting of 13 families. Distribution of fish species along Juwana River the lower diversity due uneven distribution tends to spread and there are species that dominate at each research station These valuen were influeced by criteria based on contamination levels indicate that the river is polluted Juwana in a state of mild to quite severe.