TRENTON, N.J. (AP) _ The American Cyanamid Corp. on Friday pleaded guilty to 37 acts of water pollution and agreed to pay fines totaling $900,000, the largest criminal penalty ever assessed against a New Jersey company.

The chemical manufacturer admitted discharging pesticide byproducts and waste in the Rahway River from May 1982 to November 1985 from its Linden plant, where state officials said the material was released through holes in a floor.

American Cyanamid entered the guilty pleas before Union County Superior Court Judge Miriam Span, who approved the fines.

''This fine, one of the largest imposed anywhere in the nation, demonstrates New Jersey's commitment to a clean, safe environment,'' said Attorney General W. Cary Edwards.

Company spokesman E.G. West called the discharges ''minor'' and said the fines were ''greatly disproportionate to the minor nature of the infringements.''

He said the company did acknowledge making negligent discharges at the plant.

''I'm delighted the state is taking criminal action against violators,'' said Ed Lloyd, legal counsel for New Jersey Public Interest Research Group, a citizens and environmental rights group.

Lloyd said American Cyanamid was found liable in November 1985 for 336 violations of its discharge permit at its Linden plant from 1977 to 1982, in a civil case brought in federal court by his group and Friends of the Earth.

Donald Belsole, director of the Division of Criminal Justice, said an investigation determined a floor in one of the company's buildings was built with holes leading directly to the Rahway River.

The floor routinely became contaminated with residual amounts of chemicals and wastes and rather than pumping the material into an on-site sewage treatment plant, employees washed down the floors to drain the chemicals through the holes, Belsole said.

He said the company also improperly discharged chemicals directly into the river through steam siphons and that some pollutants escaped through leaky pipes.

The responsibility was not attributed to any individual or identifiable group in the company, Edwards said.

''Rather, the pollution was a result of poor housekeeping practices employed by workers ... and the company's failure to upgrade the plant's physical facilities,'' he said.

Edwards said an investigation by the Department of Environmental Protection determined that no permanent environmental harm occurred, and that a cleanup is not required.

But the company has agreed to make extensive capital improvements at the plant to prevent further pollution, he said.

''It is our intention to send a loud and clear message to all companies doing business in the state that we will not tolerate any illegal discharge of wastes into our waterways,'' Edwards said.