Nipsa, Unite and GMB members voted last month for a work-to-rule and withdrawal of on-call services and overtime.
Water supply to about 10,000 customers in counties Fermanagh and Tyrone was disrupted over the weekend.
The company said one of five pumps at its Enniskillen treatment plant broke down, and industrial action meant repairs were delayed.
The disruption continued to affect hundreds of customers on Monday.
Agreement was reached before Christmas to provide some emergency cover, but following talks facilitated by the Labour Relations Agency last week, unions rejected an offer made by management on Friday.
NI Water made proposals for changes to its pension scheme last July.
Unions say increased pension contributions could cost members up to Â£100 a month, and they want this to be offset by an increase in salaries.
They also want pension changes to be delayed for a year until April 2016.
NI Water say increased contributions for most staff would be much less than the Â£100 claimed by the union, and any pay deal would have to include changes to some working practices, including longer working days for some staff.
Northern Ireland Water and trade unions are to hold further talks later to resolve a pensions dispute.