The villages of Rasce, Radusa, Dolno Lisice and Zelenikovo near the Macedonian capital faced flooding.
According to the Crisis Management Center, the Rasce water source for the Skopje supply system is not in jeopardy.
The rivers Treska and Zirovnicka have also flooded villages in the the Kicevo and Mavrovo regions, respectively.
The villages of Raotince, Kopance and Tudence in the municipality of Jegunovce are the most seriously affected in the northwest of the country, with reports that some 130 houses and over 250 hectares of arable land have been flooded.
The flood has been attributed to the increased water levels in the Vardar tributaries, Pena, Poroj, Neprostenska and Bogovinje, which were caused by the heavy rain showers that hit the region in the last few days. This caused the Vardar to spill over its banks at critical points.
The river has been causing headaches for local residents since Friday when its levels first rose and then later subsided. Fluctuations in the water level continued throughout the week, and residents and the authorities were on constant alert.
Macedonian Prime Minister Nikola Gruevski, Jegunovce municipality officials as well as officials from the national crisis management centre have toured the region and promised help.
They say the situation is being constantly monitored.
Both communities in Kosovo blame politics for the trial of Fatmir Limaj - though from diametrically opposing points of view.