The Edinburgh-based firm admitted to one environmental offence for an unauthorised discharge of water before Leeds Crown Court on Wednesday, 18 May.
The housing developer was fined £100,000 with over £2,901 in costs.
In addition, Flannery Civil Engineering Ltd, of Willow Bridge Way, Castleford, was fined £9,000 by Kirklees Magistrates' Court in March after admitting a similar charge for its involvement in the same incident.
The court heard how water discharge containing silt and sediment ran from a construction site into a watercourse at Lindley Park, Huddersfield in November 2013.
The polluted water was discharged into a nearby watercourse that runs into Grimescar Dyke.
Miller Homes had contracted Flannery to develop four storage lagoons in order to reduce the risk of flooding downstream.
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Straw bales were used on the outflow of the lower lagoon to prevent silt from leaving the site.
However due to heavy rainfall, the lower lagoon filled with water, and Flannery removed the straw bales to allow it to drain. With the bales removed, silt water ran directly into the watercourse, affecting water quality.
A member of the public reported the incident to the Environment Agency (EA), which sent an officer who discovered the watercourse was running a dark brown colour, and traced the source back to the development site.
In addition, the officer saw that the straw bales were situated at the side of the lagoon, no longer filtering the discharge. Water entering the top lagoon was clear, but the water leaving the bottom lagoon was cloudy.
In mitigation, Miller Homes said they immediately improved the lagoon system following the incident, adding they are one of a small number of house building companies which have achieved an accreditation for environmental standards.
It added their board of directors had been "apoplectic" that the problem had not been reported to the Environment Agency or even themselves at the time.
An EA spokesperson said: "Environmental permitting laws exist to protect the environment and local communities from harm. This case shows how important it is that construction and other industrial companies adhere to the regulations to ensure that their activities do not pose a risk of pollution.
"Miller Homes should have had more effective water management systems on the construction site to prevent the silty run-off from affecting local watercourses."
(LM)
