In a medium saucepan, bring the clam juice and water to a simmer.
In a large pot, cook the bacon until crisp.
Remove the bacon from the pot and pour off all the fat. In the same pot, heat the oil over moderately low heat. Add the onion and garlic and cook, stirring occasionally, until the onion is translucent, about 5 minutes.
Add the rice to the pot and stir until it begins to turn opaque, about 2 minutes. Add the wine and salt and cook, stirring frequently, until all the wine has been absorbed.
Add the bacon and about 1/2 cup of the simmering clam juice to the rice and cook, stirring frequently, until the liquid has been completely absorbed. The rice and liquid should bubble gently; adjust the heat as needed.
Continue cooking the rice, adding clam juice 1/2 cup at a time and allowing the rice to absorb the liquid before adding the next 1/2 cup. Cook the rice in this way until tender, 25 to 30 minutes in all.
The liquid that hasn't been absorbed should be thickened by the starch from the rice. You may not need to use all of the clam juice, or you may need to add some water.
Stir in the chives, pepper, and clams. Cook, stirring, until the clams are just done, about 1 minute. Taste for salt and add more salt if needed.