A heat exchanger is cleaned, inspected and/or plugged while the heat exchanger is in operation. In some embodiments, the heat exchanger includes a channel cover having valve-seal assemblies allowing isolation tools to be inserted through the channel cover into sealing engagement with the ends of tubes to provide a flow path separate from the normal flow paths through the heat exchanger. Cleaning and/or inspecting can be done through the isolation tools and tubes that are leaking can be plugged through the valve-seal assemblies. In some embodiments, brushes are located inside the heat exchanger and can be independently advanced into cleaning relation with a large majority of the tubes.