Site worker David Farrow received internal injuries and a broken pelvis in the incident where the company was installing a septic tank system.
The company had pleaded guilty to health and safety breaches at an earlier hearing at Wrexham Magistrates’ Court.
HSE inspector Debbie John said: "Construction has a significant number of risks to health and safety which need to managed properly.
“There was a systematic failure by Winnington Construction to manage the risk on this site, which resulted in Mr Farrow falling into the excavation and receiving quite serious injuries."
The firm was also ordered to pay £12,000 in costs.