| Sparidae | Acanthopagrus berda | Picnic seabream | native |
| Apogonidae | Apogon hyalosoma | Humpbacked cardinalfish | native |
| Cyprinidae | Aristichthys nobilis | Bighead carp | introduced |
| Ariidae | Arius subrostratus | Shovelnose sea catfish | native |
| Ariidae | Arius sumatranus | Goat catfish | native |
| Bagridae | Bagroides melapterus | native |
| Cyprinidae | Balantiocheilos melanopterus | Tricolor sharkminnow | native |
| Cyprinidae | Barbichthys laevis | Sucker barb | native |
| Cyprinidae | Barbodes collingwoodii | native |
| Cyprinidae | Barbonymus schwanenfeldii | Tinfoil barb | native |
| Osphronemidae | Betta macrostoma | Spotfin betta | native |
| Gobiidae | Boleophthalmus boddarti | Boddart's goggle-eyed goby | native |
| Gobiidae | Brachygobius doriae | native |
| Gobiidae | Calamiana illota | native |
| Chacidae | Chaca bankanensis | Angler catfish | native |
| Channidae | Channa melasoma | Black snakehead | native |
| Cyprinidae | Chela maassi | native |
| Clupeidae | Corica soborna | Ganges river sprat | native |
| Cyprinidae | Crossocheilus cobitis | native |
| Cyprinidae | Ctenopharyngodon idella | Grass carp | native |
| Cyprinidae | Cyclocheilichthys microlepis | native |
| Cyprinidae | Cyprinus carpio carpio | Common carp | introduced |
| Hemiramphidae | Dermogenys bruneiensis | native |
| Syngnathidae | Doryichthys deokhatoides | native |
| Syngnathidae | Doryichthys martensii | native |
| Gobiidae | Eugnathogobius oligactis | native |
| Gobiidae | Eugnathogobius siamensis | native |
| Cyprinidae | Garra borneensis | native |
| Balitoridae | Gastromyzon aeroides | native |
| Balitoridae | Gastromyzon borneensis | native |
| Balitoridae | Gastromyzon cranbrooki | native |
| Balitoridae | Gastromyzon lepidogaster | native |
| Balitoridae | Gastromyzon venustus | native |
| Carcharhinidae | Glyphis glyphis | Speartooth shark | native |
| Cyprinidae | Hampala ampalong | native |
| Cyprinidae | Hampala bimaculata | native |
| Bagridae | Hemibagrus baramensis | native |
| Gobiidae | Hemigobius hoevenii | native |
| Balitoridae | Homaloptera ophiolepis | native |
| Pristigasteridae | Ilisha megaloptera | Bigeye ilisha | native |
| Sciaenidae | Johnius borneensis | Sharpnose hammer croaker | native |
| Sciaenidae | Johnius coitor | Coitor croaker | native |
| Siluridae | Kryptopterus lais | native |
| Siluridae | Kryptopterus limpok | native |
| Siluridae | Kryptopterus macrocephalus | Striped glass catfish | native |
| Latidae | Lates calcarifer | Barramundi | native |
| Cyprinidae | Leptobarbus hosii | native |
| Mugilidae | Liza subviridis | Greenback mullet | native |
| Cyprinidae | Lobocheilos falcifer | native |
| Cyprinidae | Luciosoma spilopleura | Apollo sharkminnow | native |
| Cyprinidae | Luciosoma trinema | native |
| Lutjanidae | Lutjanus argentimaculatus | Mangrove red snapper | native |
| Mastacembelidae | Macrognathus maculatus | Frecklefin eel | native |
| Bagridae | Mystus castaneus | native |
| Balitoridae | Nemacheilus longipectoralis | native |
| Balitoridae | Nemacheilus olivaceus | native |
| Cyprinidae | Nematabramis steindachneri | native |
| Phallostethidae | Neostethus bicornis | native |
| Phallostethidae | Neostethus borneensis | native |
| Phallostethidae | Neostethus lankesteri | native |
| Siluridae | Ompok eugeneiatus | native |
| Siluridae | Ompok jaynei | native |
| Siluridae | Ompok leiacanthus | native |
| Siluridae | Ompok platyrhynchus | native |
| Cichlidae | Oreochromis niloticus niloticus | Nile tilapia | introduced |
| Cyprinidae | Osteochilus enneaporus | native |
| Cyprinidae | Osteochilus harrisoni | native |
| Cyprinidae | Osteochilus spilurus | native |
| Cyprinidae | Osteochilus triporos | native |
| Cyprinidae | Osteochilus waandersii | native |
| Eleotridae | Oxyeleotris marmorata | Marble goby | native |
| Cobitidae | Pangio agma | native |
| Cobitidae | Pangio mariarum | native |
| Cyprinidae | Parachela hypophthalmus | native |
| Cyprinidae | Parachela oxygastroides | Glass fish | native |
| Cyprinidae | Paracrossochilus acerus | native |
| Cyprinidae | Paracrossochilus vittatus | native |
| Balitoridae | Parhomaloptera microstoma | native |
| Pristigasteridae | Pellona ditchela | Indian pellona | native |
| Balitoridae | Protomyzon aphelocheilus | native |
| Balitoridae | Protomyzon borneensis | native |
| Balitoridae | Protomyzon griswoldi | native |
| Balitoridae | Protomyzon whiteheadi | native |
| Bagridae | Pseudomystus fuscus | native |
| Bagridae | Pseudomystus inornatus | native |
| Siluridae | Pterocryptis furnessi | native |
| Cyprinidae | Puntioplites waandersi | native |
| Cyprinidae | Puntius binotatus | Spotted barb | native |
| Cyprinidae | Rasbora argyrotaenia | Silver rasbora | native |
| Cyprinidae | Rasbora borapetensis | Blackline rasbora | native |
| Cyprinidae | Rasbora einthovenii | Brilliant rasbora | native |
| Cyprinidae | Rasbora kottelati | native |
| Cyprinidae | Rasbora trifasciata | native |
| Cyprinidae | Rasbora tubbi | native |
| Sillaginidae | Sillago sihama | Silver sillago | native |
| Siluridae | Silurichthys marmoratus | native |
| Siluridae | Silurichthys phaiosoma | native |
| Cobitidae | Syncrossus reversa | native |
| Clupeidae | Tenualosa macrura | Longtail shad | native |
| Cyprinidae | Thynnichthys thynnoides | native |
| Cyprinidae | Tor tambra | native |
| Balitoridae | Vaillantella euepiptera | native |
| Balitoridae | Vaillantella maassi | native |