There was no immediate Brazilian reaction to Mujica's surprise precondition for the inspection, which forms part of Argentine-Uruguay agreements on ending an international dispute on an eucalyptus pulp mill operated by Uruguay and opposed by environmentalists.
Argentina opposed the mill on the Uruguyan side of the river and took the matter to the International Court of Justice in The Hague, Netherlands. It lost the case against the mill and against Uruguay and made peace with its neighbor in expectation of lucrative trade deals.
In the meantime, however, anti-mill campaigners encouraged by Argentina during a four-year campaign took on an independent role, refusing to end their protests.
A compromise reached this week will see the protesters suspending their blockade of the bridge linking Argentina and Uruguay over the river for 60 days. They promised to resume their blockade if they did not get rights to inspect the mill and monitor its waste disposal into the river.
Uruguay denies the mill is a pollutant, a position accepted by the court after scientific evaluations and expert reports from the Finnish firm that installed the mill.
Mujica's proposal indicated a hardening of the Uruguay position and an escalation that could also embarrass Brazil because the river originates near Bage, in Brazil.
"I think the next step is for a three-country monitoring process to ensure the river Uruguay does not contaminate and is not contaminated, and I mean Brazil where the river also covers quite a distance and brings along some things from the hinterland," said Mujica.
The Uruguayan president described the activists' decision to temporarily lift the blockade of the bridge as "quite positive." Even if it is for 60 days, he said, the compromise represented progress.
He called the temporary accord "the fourth goal on a sky-blue day," a reference to Uruguay's 3-0 win over South Africa in the World Cup and the colors of the national team.
Mujica's comment means that if an inspection of the river water does take place, it will take into account all pollutants including any flowing down from Brazil, analysts said.
The pollution of water in Brazil's rivers and streams is already a hot issue, but now it has been brought into focus in an unexpected way and could produce unpredictable political results for all three countries -- Argentina, Uruguay and finally Brazil, analysts said.
Uruguayan officials also want to take a closer look at Argentine use of the river.
The protesters' decision to lift the blockade for 60 days followed Argentina's threat of prosecution of about 20 of the activists.
The decision to bring civil and criminal charges against the activists stemmed from increasing irritation expressed by Argentine President Cristina Fernandez de Kirchner over the protesters' defiance and their independence.
Argentine officials who previously felt confident of control over the protesters' action felt let down and angry with the protesters, media reports said.
The protesters now want the charges dropped as part of any deal to end the blockade when the 60-day suspension period expires.
Mujica said when the inspections of the river water and the pulp mill start he would expect science to rule over politics.
Mujica said he wanted standard procedures in place for the monitoring "which we will apply all along the river. That's where Brazil comes in. We want to prove we have nothing to hide, nothing to conceal, so now the job is to agree on how to monitor the whole water course, not only in Fray Bentos" -- the Uruguay town where the pulp mill is located.
Both Argentina and Brazil have industries further up the river with few controls on waste disposal into the river waters.