CLRS chief executive Leah Taaffe said her team had been forced to suspend certain programs during the six-week lockdown.
“We will have to suspend our community activities and recyclability,” she said.
“We will have to close the op-shop down as well for the time being. But fortunately we will be able to continue to offer one-to-one support for anyone who requires it, as well as finding ways to offer other kinds of support.”
Ms Taaffe said it would be a major blow for many.
“It's a mental challenge for people knowing so many of the activities we normally would run can't happen,” she said.
“We had just started to get back to a number of those activities, and unfortunately now they are on hold once again.
“Currently we are working with our clients and trying to figure out what we can do differently and how we can continue to provide the support for them in other ways.”
The NSW-Victorian border closing also caused havoc for the Murray River Tea Rooms, which CLRS runs.
Both staff and clients were initially ineligible for border permits.
“We had some real difficulties with both our clients and our staff due to the border permit,” she said.
“The first set of restrictions weren't a major issue, but when the second changes were made it became really difficult for people to get across the border to work in the tea rooms.
“The (NSW) government then introduced some new rules and made it a lot easier. There are always issues when these type of changes are made, and unfortunately we were disadvantaged in the initial stages.
“The restrictions were confusing and very unclear to begin with, the tweaks were made around the edges to make it useable, and for that we are grateful to advocacy groups, organisations and politicians for their commitment to get it changed.
“The improvements made in the past two weeks have made it fare better.”
But CLRS said it was prepared for another lockdown.
“Since March we have been having regular meetings as an organisation,” she said.
“We've been trying to identify as many possible issues as we could, looking at what may come up in the coming months with COVID-19 and how we might be able to deal with them.
“When a major change like stage three, as difficult as it is going to be comes along, we are ready to respond and do what we need to do to keep things moving and operating as best as we can.
“We are regularly communicating with clients and staff about what might happen, so when it arises no-one is caught off guard, we are ready to go and everyone understands what is going to happen.”
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