The performance of higher order modulation formats such as 16-quadrature amplitude modulation (QAM) coherent optical communication systems are limited due to several linear and nonlinear impairments such as phase noise, frequency offset, chromatic dispersion, and fiber nonlinearities. For a satisfactory system performance, these impairments need to be eliminated either by all-optical and/or electronic means. In this paper, we use the extended Kalman filter (EKF) algorithm to jointly mitigate laser phase noise, frequency offset, and nonlinear channel impairments, namely self phase modulation and nonlinear phase noise in polarization multiplexed 400 Gb/s 16-QAM and 200 Gb/s quadrature phase shift keying (QPSK) systems. We consider a two-state EKF with phase as one state and frequency offset as another. Simulation results for transmission over 1000 km (10 × 100 km) of standard single mode fiber show a Q-factor of 12 dB for PM-16-QAM at frequency offset of 1 GHz and laser linewidth of 100 kHz and a Q-factor of 18 dB for PM-QPSK at 1 MHz linewidth. Further, phase trajectories corresponding to tracked laser phase noise and frequency offset show that EKF can suppress laser phase noise up to 10 MHz and frequency offset up to 5 GHz, thereby eliminating the requirement of using separate algorithms for phase noise and frequency offset estimation.