Pot experiment were conducted from 2013 to 2014 to provide solutions for poor water–nitrogen (N) use efficiency with zeolite (Z) in near-surface soil. This article aims to study the influences of different levels of Z (Z1, Z2, Z3, 0, 7500, and 15,000 kg hm−2) and N (N1, N2, N3, 0, 78.75, and 157.5 kg hm−2) on rice grain yield, soil total N (STN), water productivity (WP), and N recovery efficiency (NRE). Results showed that higher dry matter weight, grain yield, water consumption, N accumulation, and WP were obtained with increasing N rates. There were no significant influences on dry matter weight of stem and leaf, water consumption, and WP with the application of Z. However, Z input could obtain a higher spike and root weight, grain yield, 1000-grain weight, N accumulation, STN, and NRE. Z might alleviate the water used in jointing-booting stage, heading-flowering stage, and milky ripen stage. Overuse of Z and N led to a decrease in NRE. N3Z2 increased rice grain yield by 10.4%, WP by 7.3%, and NRE by 63% compared with conventional fertilization (N3Z1). The way of N3Z2 is recommended to improve rice yield, WP, NRE, and STN comprehensively in coastal region of Northeast China.