The limnological properties and phytoplankton as pollution indicator was studied for three Months between February and April,2022. Water and phytoplankton samples were collected from three stations following standard method of APHA using 45µm mesh size plankton net and plastic bottles for phytoplankton and physicochemical variables respectively. The results showed that some of the physicochemical variables studied had their mean values, pH (6.23±0.69), dissolved oxygen (DO)(5.60±0.11 mg/l), electrical conductivity (EC)(280.00±7.0 µs/cm), sulphate (SO4) (83.00±1.00 mg/l) and turbidity(4.91±0.43 cm) within the permissible limits of WHO while others were above the limits. The results also showed that all the variables did not show significant difference spatially at p<0.05 except BOD, EC and NO3. Most of the variables recorded the highest values in March except NO3 with SO4 and NO3 recording the highest values in station 2. A total number of 31 species of phytoplankton belonging to the five taxonomic groups in the order, bacillariophyceae, cholorophyceae, cyanophyceae, chrysophyceae and xanthophyceae were identified. Phytoplankton species identified to be pollution indicator species were Navicular sigma, Cyclotella combata, Cyclotella operculata, Spirogyra sp, Anabaena affinis, Anabaena flus-aqua, Microcystis pulvenca, and Oscillaria lacustris. The total abundance of phytoplankton was highest in station 2 (1,508 Ind/ml) but lowest in station 1(1,144 Ind/ml). Considering the values of some of the physicochemical variables which were above the permissible limits of WHO and the occurrence of some pollution indicator species, Choba segment of the New Calabar River is considered to be at the verge of been threatened/polluted. Therefore, adequate measures should be put in place to regulate the anthropogenic activities in the area.